The lower Cambrian and lower Silurian shale reservoirs of southern China display significant differences in pore characteristics that may reflect the varying effects of silica diagenesis. The lower Cambrian and lower Silurian mudstone samples from the middle–upper Yangtze platform were analyzed to elucidate silica diagenetic modifications, including their influences on pore evolution. Quartz of the studied mudstone samples includes detrital quartz, overgrowths, siliceous skeletal fragments, microquartz aggregates, silica nanospheres, and matrix-dispersed microquartz. Much of the authigenic silica precipitated in association with diagenetic alteration of the studied deposits appears to have been derived from dissolution of siliceous skeletal fragments and the smectite–illite reaction. A paucity of siliceous organisms populating the early Cambrian ocean gave rise to more complicated silica diagenetic pathways during alteration. Silica precipitation from silica-rich seawater/pore water and silica replacement by carbonate/carbonate-fluorapatite may have supplemented diagenetic modification of lower Cambrian mudstone. The species types of organisms that contributed skeletal grains to the sediments and the amount of precipitated authigenic quartz appear to have impacted organic pore evolution. The abundance of early Cambrian benthic siliceous sponge spicules appears to have muted formation of rigid microquartz aggregates and silica nanospheres that would have shielded organic pores. In contrast, the early Silurian bloom of planktonic radiolarians was associated with accumulation of organic-rich siliceous mudstone and the formation of abundant microquartz aggregates and silica nanospheres that shielded organic pores during burial. In summary, the amount and type of diagenetic quartz influenced pore characteristics of lower Cambrian and lower Silurian shale reservoir rocks of southern China.